Molecular modeling of the neurophysin I/oxytocin complex

Neurophysins I and II (NPI and NPII) act in the neurosecretory granules as carrier proteinsfor the neurophyseal hormones oxytocin (OT) and vasopressin (VP), respectively. The NPI/OTfunctional unit, believed to be an (NPI/OT)2 heterotetramer, was modeled using low-resolution structure information, viz. the C carbon atom coordinates of the homologousNPII/dipeptide complex (file 1BN2 in the Brookhaven Protein Databank) as a template. Itsall-atom representation was obtained using standard modeling tools available within theINSIGHT/Biopolymer modules supplied by Biosym Technologies Inc. A conformation of theNPI-bound OT, similar to that recently proposed in a transfer NOE experiment, was dockedinto the ligand-binding site by a superposition of its Cys1-Tyr2 fragment onto the equivalentportion of the dipeptide in the template. The starting complex for the initial refinements wasprepared by two alternative strategies, termed Model I and Model II, each ending with a100 ps molecular dynamics (MD) simulation in water using the AMBER 4.1 force field. The freehomodimer NPI2 was obtained by removal of the two OT subunits from their sites, followedby a similar structure refinement. The use of Model I, consisting of a constrained simulatedannealing, resulted in a structure remarkably similar to both the NPII/dipeptide complex anda recently published solid-state structure of the NPII/OT complex. Thus, Model I isrecommended as the method of choice for the preparation of the starting all-atom data forMD. The MD simulations indicate that, both in the homodimer and in the heterotetramer, the310-helices demonstrate an increased mobility relative to the remaining body of the protein.Also, the C-terminal domains in the NPI2 homodimer are more mobile than the N-terminalones. Finally, a distinct intermonomer interaction is identified, concentrated around its mostprominent, although not unique, contribution provided by an H-bond from Ser25O in one NPI unit to Glu81 O in the other unit. This interaction is present in the heterotetramer(NPI/OT)2 and absent or weak in the NPI2 homodimer. We speculate that this interaction,along with the increased mobility of the 310-helices and the carboxy domains, may contributeto the allosteric communication between ligand binding and NPI dimerization.     

Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation

The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. Therefore, there is increased interest in screening compounds that can inhibit influenza virus RNA polymerase. Three natural compounds were found by using molecular docking-based virtual screening, which could bind tightly within the polymerase acidic protein-polymerase basic protein 1 (PA-PB1) subunit of influenza virus polymerase. Firstly, their drug likeness properties were evaluated, which showed that the hepatotoxicity values of all the three compounds indicating they had less or no hepatotoxicity, and did not have the plasma protein biding (PPB) ability, the three compounds needed to be modified in some aspects, like bulky molecular size. The stability of the complexes of PA-hits was validated through molecular dynamics (MD) simulation, revealing compound 2 could form more stable complex with PA subunit. The torsional conformations of each rotatable bond of the ligands in PA subunit were also monitored, to investigate variation in the ligand properties during the simulation, compound 3 had fewer rotatable bonds, indicating that the molecule had stronger rigidity. The bar charts of protein–ligand contacts and contacts over the course of trajectory showed that four key residues (Glu623, Lys643, Asn703 and Trp706) of PA subunit that participated in hydrogen-bond, water bridge and hydrophobic interactions with the hit compounds. Finally, the binding free energy and contributed energies were calculated by using MM-GBSA method. Out of the three compounds, compound 1 showed the lowest total binding free energy. Among all the interactions, the contribution of the covalent binding and the van der Waals energy were more than other items, compound 1 formed more stable hydrogen bonds with the residues of PA subunit binding pocket. This study smoothed the path for the development of novel lead compounds with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of influenza, which provided a good basis for further research on novel and effective influenza virus PA-PB1 interaction inhibitors.     

Molecular modeling and dynamics of neuropeptide Y

Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics     

Molecular modeling to rationalize ligand-support interactions in affinity chromatography

The development of rational design criteria for synthetic-ligand-based affinity chromatography requires a basic comprehension of all the factors influencing the binding capacity and selectivity of the stationary phase. In this work, molecular dynamics simulations are systematically used to investigate the impact of structural modifications of spacer and ligand on ligand-support interactions. The investigated ligands are characterized by a triazine core bi-functionalized with two amino acid side chains aimed at representing a range of hydrophobic/hydrophilic characters. As spacers both literature (1-2-diaminoethane and 1,4-substituted [1,2,3]-triazole) and speculative oligopeptidic molecules (Gly-[Ala]4-Gly, Gly-[Lys]4-Gly, and Gly-[Glu]4-Gly) have been considered to address the role of charges distribution, rigidity, and structural complexity. In this investigation, the spacer emerged as a key component: on the one hand, the choice of a proper spacer allows improving the hydrophilic character of the ligand-spacer adduct without compromising the structure of the affinity ligand, while on the other hand the use of structurally complex spacers induces spacer-support interactions that enhance the degree of solvation of the ligand regardless of its hydrophobic character. These findings suggest that the use of structured spacers could represent a viable pathway for tailoring the performances of affinity chromatography stationary phases.     

细菌化学趋向性受体聚集体的相互作用

细菌化学趋向性受体的最小结构单元为二聚体,在细胞膜上这些二聚体会聚集成大团簇. X射线晶体结构和低分辨电镜结构测定表明,这些团簇有两类不同的形式,一种是在晶体结构中观察到的倒金字塔式二聚体的三聚体重复形成的聚集,另一种为由二聚体尾部相互盘绕形成的拉链状聚集. 有关拉链状聚集的详细分子模型目前尚不清楚. 本文使用蛋白质-蛋白质对接的方法研究了大肠杆菌丝氨酸化学趋向性受体Tsr 二聚体之间的相互作用. 分子对接计算表明,倒金字塔式聚集和拉链状聚集的基本复合物都是可以出现的,相应复合物的分子动力学模拟表明这些结构都具有一定的稳定性. 对于所获得的拉链状聚集体的基本复合物结构模型进行了详细的二聚体作用界面分析,发现二聚体间主要通过静电和疏水作用形成复合物,其中Arg388、Phe373 和Ile377是形成拉链状聚集的关键作用残基. 所建立的Tsr 拉链状聚集的结构模型有助于揭示细菌化学趋向性受体在细胞膜上聚集的分子机制,为进一步的聚集理论及模拟研究提供了基础.     

Molecular modeling of Protein A affinity chromatography

The properties of the complex between fragment B of Protein A and the Fc domain of IgG were investigated adopting molecular dynamics with the intent of providing useful insight that might be exploited to design mimetic ligands with properties similar to those of Protein A. Simulations were performed both for the complex in solution and supported on an agarose surface, which was modeled as an entangled structure constituted by two agarose double chains. The energetic analysis was performed by means of the molecular mechanics Poisson Boltzmann surface area (MM/PBSA), molecular mechanics generalized Born surface area (MM/GBSA), and the linear interaction energy (LIE) approaches. An alanine scan was performed to determine the relative contribution of Protein A key amino acids to the complex interaction energy. It was found that three amino acids play a dominant role: Gln 129, Phe 132 and Lys 154, though also four other residues, Tyr 133, Leu 136, Glu 143 and Gln 151 contribute significantly to the overall binding energy. A successive molecular dynamics analysis of Protein A re-organization performed when it is not in complex with IgG has however shown that Phe 132 and Tyr 133 interact among themselves establishing a significant π–π interaction, which is disrupted upon formation of the complex with IgG and thus reduces consistently their contribution to the protein–antibody bond. The effect that adsorbing fragment B of Protein A on an agarose support has on the stability of the protein–antibody bond was investigated using a minimal molecular model and compared to a similar study performed for a synthetic ligand. It was found that the interaction with the surface does not hinder significantly the capability of Protein A to interact with IgG, while it is crucial for the synthetic ligand. These results indicate that ligand–surface interactions should be considered in the design of new synthetic affinity ligands in order to achieve results comparable to those of Protein A right from the ligand design stage.     

Molecular Structure of 1,2,4,5-Tetracyanobenzene from Gas-Phase Electron Diffraction and Theoretical Calculations

The molecular structure of 1,2,4,5-tetracyanobenzene has been determined by gas-phase electron diffraction and by ab initio calculations at several levels of theory. The electron diffraction study indicates an elongation of the aromatic ring along the (H)CC(H) axis, characterized by angular deformation of the benzene ring and lengthening of the (NC)C—C(CN) bonds. The following bond lengths (r _g) and bond angles were obtained by electron diffraction: .     

细菌化学趋向性受体聚集体的相互作用

细菌化学趋向性受体的最小结构单元为二聚体,在细胞膜上这些二聚体会聚集成大团簇.X射线晶体结构和低分辨电镜结构测定表明,这些团簇有两类不同的形式,一种是在晶体结构中观察到的倒金字塔式二聚体的三聚体重复形成的聚集,另一种为由二聚体尾部相互盘绕形成的拉链状聚集.有关拉链状聚集的详细分子模型目前尚不清楚.本文使用蛋白质-蛋白质对接的方法研究了大肠杆菌丝氨酸化学趋向性受体Tsr二聚体之间的相互作用.分子对接计算表明,倒金字塔式聚集和拉链状聚集的基本复合物都是可以出现的,相应复合物的分子动力学模拟表明这些结构都具有一定的稳定性.对于所获得的拉链状聚集体的基本复合物结构模型进行了详细的二聚体作用界面分析,发现二聚体间主要通过静电和疏水作用形成复合物,其中Arg388、Phe373和Ile377是形成拉链状聚集的关键作用残基.所建立的Tsr拉链状聚集的结构模型有助于揭示细菌化学趋向性受体在细胞膜上聚集的分子机制,为进一步的聚集理论及模拟研究提供了基础.     

The crystal structure of LaIr4B4, ThOs4B4, ThIr4B4 (NdCo4B4-type) and URu4B4, UOs4B4 (LuRu4B4-type)

The crystal structure of LaIr₄B₄ has been refined from single crystal counter data. LaIr₄B₄ is tetragonal,P4₂/n,Z=2, isotypic with NdCo₄B₄, |F|/|F _o|=0.039 for 312 independent reflections [|F _o|>2 (F _o)]. ThIr₄B₄ and ThOs₄B₄ also belong to the NdCo₄B₄-type structure. URu₄B₄ and UOs₄B₄ were found to crystallize with LuRu₄B₄-type structure. The crystal chemistry of (RE)T ₄B₄-phases is discussed and simple geometric relations are shown to exist between them.Dedicated to Prof.B. T. Matthias in celebration of his 60th birthday.     

Molecular modeling of cytochrome P450 3A4

The three-dimensional structure of human cytochrome P450 3A4 was modeled based on crystallographic coordinates of four bacterial P450s: P450 BM-3, P450cam, P450terp, and P450eryF. The P450 3A4 sequence was aligned to those of the known proteins using a structure-based alignment of P450 BM-3, P450cam, P450terp, and P450eryF. The coordinates of the model were then calculated using a consensus strategy, and the final structure was optimized in the presence of water. The P450 3A4 model resembles P450 BM-3 the most, but the B helix is similar to that of P450eryF, which leads to an enlarged active site when compared with P450 BM-3, P450cam, and P450terp. The 3A4 residues equivalent to known substrate contact residues of the bacterial proteins and key residues of rat P450 2B1 are located in the active site or the substrate access channel. Docking of progesterone into the P450 3A4 model demonstrated that the substrate bound in a 6-orientation can interact with a number of active site residues, such as 114, 119, 301, 304, 305, 309, 370, 373, and 479, through hydrophobic interactions. The active site of the enzyme can also accommodate erythromycin, which, in addition to the residues listed for progesterone, also contacts residues 101, 104, 105, 214, 215, 217, 218, 374, and 478. The majority of 3A4 residues which interact with progesterone and/or erythromycin possess their equivalents in key residues of P450 2B enzymes, except for residues 297, 480 and 482, which do not contact either substrate in P450 3A4. The results from docking of progesterone and erythromycin into the enzyme model make it possible to pinpoint residues which may be important for 3A4 function and to target them for site-directed mutagenesis.     

分子信标用于不对称PCR检测乙型肝炎病毒

为了缓解竞争杂交对分子信标检测的影响，将分子信标与不对称聚合酶链式反应(PCR)联用进行血清中乙型肝炎病毒(HBV)的检测。并采用更为直接的荧光方法，将不对称PCR扩增中的引物浓度比确定为5：1，该结果与电泳方法得到的结果有所不同。文中结合对称及不对称PCR过程中荧光强度的变化情况，对其原因进行了详细的探讨。分子信标与不对称PCR联用，可以专一地检测出血清中HBV的存在，与分子信标／对称PCR相比．其检测效果明显增强。     

Molecular dynamics investigation of the pressure induced B1 to B2 phase transitions of RbBr

The pressure induced transformation of rubidium bromide from the NaCl (B1) to the CsCl (B2) type structure is elucidated by means of molecular dynamics simulations. Two different approaches were followed. The “conventional” procedure of applying pressures, which are increased successively, leads to a phase transformation at a critical pressure of 80-85 kbar. This is 16-17 times the experimental value. On the other hand, the phase transition is studied by path sampling molecular dynamics simulations. This approach allows investigating the process at 5 kbar, i.e. it does not require over-driving. At this pressure the system takes pathways related to the route proposed by Bürger, exclusively. In the runs in which an over-pressurization of 80 kbar is applied, we instead observe both the Bürger mechanism and the route proposed by Watanabe et al.     

Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding

Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.     

Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein–DNA interaction

Molecular dynamics simulation of Escherichia coli trp-repressor/operator complex was performed to elucidate protein–DNA interactions in solution for 800 ps on special-purpose computer MD-GRAPE. The Ewald summation method was employed to treat the electrostatic interaction without cutoff. DNA kept stable conformation in comparison with the result of the conventional cutoff method. Thus, the trajectories obtained were used to analyze the protein–DNA interaction and to understand the role of dynamics of water molecules forming sequence specific recognition interface. The dynamical cross-correlation map showed a significant positive correlation between the helix-turn-helix DNA-binding motifs and the major grooves of operator DNA. The extensive contact surface was stable during the simulation. Most of the contacts consisted of direct interactions between phosphates of DNA and the protein, but several water-mediated polar contacts were also observed. These water-mediated interactions, which were also seen in the crystal structure (Z. Otwinowski, et al., Nature, 335 (1998) 321) emerged spontaneously from the randomized initial configuration of the solvent. This result suggests the importance of the water-mediated interaction in specific recognition of DNA by the trp-repressor, consistent with X-ray structural information.     

Molecular modeling and structural analysis of some tetrahydroindazole and cyclopentanepyrazole derivatives as COX-2 inhibitors

In an attempt to rationalize the search for new potential anti-inflammatory compounds on the COX-2 enzyme, we carried out an in silico protocol that successfully combines the prediction of physicochemical and pharmacokinetic properties, molecular docking, molecular dynamic simulation, and free energy calculation. Starting from a small library of compounds synthesized previously, it was found that 70% of the compounds analyzed satisfy with the associated values to physicochemical principles as key evaluation parameters for the drug-likeness; all the compounds presented good gastrointestinal absorption and cerebral permeability and they showed an interaction with the Arg 106 residue of the COX-2 isoenzyme. Finally, it was obtained that compound 3ab has a binding mode, binding energy, and stability in the active site of COX-2 like the reference drug celecoxib, suggesting that this compound could become a powerful candidate in the inhibition of the COX-2 enzyme. In addition, we realized the crystallographic analysis of compounds 3j, 3r, and 3t defining the crystal parameters and the Packing interactions.     

Folding behaviors of apocytochrome b5 and its mutants: Insights from high temperature molecular dynamics simulations

Apocytochrome b₅ (apocyt b₅) with heme removal from the heme-binding core 1, and its mutants with amino acid replaced in the hydrophobic core 2, namely apocyt b₅ Y7P, P81A and H15R/S20E, have been subjected to molecular dynamics (MD) simulation at high temperature (500 K) for elucidating their folding behaviors. The early events upon thermal induced unfolding were found to be in good agreement with available experimental results, and the lowest stability of Y7P was predicted among the four apoproteins. The influences of these key residues on protein folding behavior were compared directly at an atomic level. At the same time, the influences of non-native interactions of hydrogen bonds and salt-bridges on protein stabilities were analyzed in detail. The insights from current MD simulations are valuable for understanding the apoprotein folding and the holoprotein formation in terms of heme proteins.     

分子动力学模拟研究点突变(Met108→Leu108)对树胶醛糖结合蛋白与配体作用的影响

为了研究点突变(Met108→Leu108)对树胶醛糖结合蛋白(ABP)与配体结合能力的影响,对ABP、ABP结合树胶醛糖复合物及ABP结合半乳糖复合物以及它们各自的突变体分别进行60 ns的分子动力学模拟.模拟结果表明,108号残基突变前后,电子等排体的两个氨基酸残基,使蛋白与配体间的范德华相互作用发生明显变化,同时导致蛋白的内部运动也发生变化,进而影响蛋白与配体的相互作用.进一步分析表明,突变前后的蛋白构象变化都趋向于两个结构域张开,而与配体的结合可减缓张开程度.     

Theoretical study of the gas-phase thermolysis reaction of alkyl (ethyl,isopropyl, and tert-butyl) N,N-dimethylcarbamates and N,N-diethylcarbamates

Theoretical studies on the thermolysis in the gas phase of alkyl N,N-dialkylcarbamates were carried out using ab initio theoretical methods, at the MP2/6-31G(d), MP2/6-31++G(d,p) and MP2/6-311++G(2d,p)//MP2/6-31G(d) levels. The reactions have two steps: the first one corresponds to the formation of an alkene and a neutral dialkylcarbamic acid intermediate via a six-membered cyclic transition state; the second one is the decarboxylation of this intermediate via a four-membered cyclic transition state, leading to carbon dioxide and the corresponding dialkylamine. The progress of the reactions was followed by means of the Wiberg bond indices. The results indicate that the transition states have character intermediate between reactants and products, and the calculated synchronicities show that the reactions are slightly asynchronous. The bond-breaking processes are more advanced than the bond-forming ones, indicating a bond deficiency in the transition states. The rate constants calculated for all the reactions agree very well with the available experimental data.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)